A closed-loop coupling model at the system-level is developed to analyze the effects of joint clearance on the dynamic responses of electromechanical aileron actuation system. The proposed model considers the coupling effects between the electromechanical actuator (EMA) control performance and dynamic characteristics of linkage mechanism with joint clearance. Besides, the experiments are conducted in a test rig, which verifies the effectiveness of the proposed closed-loop coupling model. The nonlinear contact force model and modified Coulomb friction model are adopted in the joint clearance of the linkage mechanism, and the influences of clearance size on the dynamic behaviors of electromechanical aileron actuation system are studied. The numerical and experimental results indicate that the novel closed-loop coupling model, considering the EMA control performance and dynamics of linkage mechanism with joint clearance at the same time, is an effective model to predict the dynamic characteristics of electromechanical aileron actuation with joint clearance, which provides a practical method to analyze the dynamic performance of electromechanical coupling multibody systems with joint clearance.